Hello! I've been trying to perform a GWAS on my dataset using Plink. I've got a good hold on how the basic allelic test and alternate tests work but the majority of my SNPs are significant in both chi squared tests and also in all other model tests. Which makes me a bit nervous on how to interpret and comment on these results. For example SNP1 exhibits significance in basic assoc test, but also is significant when using cochran armitage, and dominant/ recessive tests. How is this interpreted and what's the significance of this result?
Any help is appreciated